Photoshop :: How Two Pictures Of Same Size Appear To Be Different Size

I called the big webdesign file "(X)" and the image I wanted to paste in it "(Y)",

What Happened:

For the design of a webpage, I made a photoshop-file(X) with a lot of squares(X). These squares(X) had the size 9,42×9,42 centimeters. I measured the squares(X) carefully and also made sure the size was in centimeters, so I am sure that the size was 9,42×9,42 cm. My plan was to fill the squares(X) with pictures(Y). I had a map on my computer with a lot of square-sized JPG-images(Y) in it. All I had to do was open the pictures(Y) in photoshop, change the size into 9,42×9,42 centimeters and copy+paste them into the squares(X) of the webdesign. I did this before and it worked perfectly.

But then, I opened one of the images(Y) and when I wanted to resize it, the resize-tool said it was only 3,25×3,25 centimeters big.I thought it was strange, so I copied+pasted it into the design-file(X) with all the squares(X) that needed to be filled. Allthough photoshop had told me that the squares(X) in the file were 9,42×9,42 centimeters big and the image(Y) I resized was 3,25×3,25, the "small" image(Y) turned out to be bigger then the squares(X). And when I resized the "small" image(Y) into 9,42×9,42 centimeters, it was even bigger than it was before. How can this be, and how can I still make the images(X&Y) the same size?
 
What I already tried:

- I made the file of the webdesign(X) with all the squares(X) into one layer, copied the file(X) and opened a new file(X) with the same measurements of the old file(X). I also changed the resolution of the file(X) into pixels/centimeters instead of pixels/inches. Then I pasted the image(X) of the old file into the new file. I didn't work; the image(X) that I pasted in the new file was bigger and when I pasted the other picture(Y) in this image, the same problem was still there.

- I also opened the picture(Y) in photoshop, made a screenshot of it and then pasted the screenshot into paint. With paint I cropped it again and saved it as a JPEG-file. After that, I opened the image (Y) in photoshop again. It now had the size of 11,27×11,27 centimeters. Then I resized the image(Y) into 9,42×9,42 cm, but it still wasn't as big as the squares(X).